Fix checked in... Off to adding NH4+ SHAKE support now (in 3 years no one
ever complained about this: Until now)...
On Wed, Jan 11, 2012 at 7:03 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
> Found it...
>
> Checking in fix shortly:
>
> GPU DPDP:
> NSTEP = 200 TIME(PS) = 200.400 TEMP(K) = 298.54 PRESS =
> 236.8
> Etot = -114607.6739 EKtot = 27373.9425 EPtot =
> -141981.6164
> BOND = 996.2311 ANGLE = 2512.1603 DIHED =
> 1647.9070
> UB = 323.5942 IMP = 159.1814 CMAP =
> -380.4425
> 1-4 NB = 922.7533 1-4 EEL = 10149.6941 VDWAALS =
> 11075.4372
> EELEC = -169388.1325 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 11764.1346 VIRIAL = 9529.6640 VOLUME =
> 436985.4968
> Density =
> 1.0467
>
> CPU:
> NSTEP = 200 TIME(PS) = 200.400 TEMP(K) = 298.53 PRESS =
> 237.0
> Etot = -114607.9710 EKtot = 27373.6615 EPtot =
> -141981.6325
> BOND = 996.2197 ANGLE = 2512.1427 DIHED =
> 1647.8892
> UB = 323.5874 IMP = 159.1712 CMAP =
> -380.4489
> 1-4 NB = 922.7679 1-4 EEL = 10149.7372 VDWAALS =
> 11074.9732
> EELEC = -169387.6720 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 11764.3560 VIRIAL = 9528.0691 VOLUME =
> 436985.2915
> Density =
> 1.0467
>
>
>
>
>
>
> On Wed, Jan 11, 2012 at 4:14 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
>
>> I'm back on this now. There were some issues at work that needed
>> attending to that led to me missing this year's AMBER conference (yet again
>> sigh)...
>>
>> I'm not exactly sure this bug isn't fixed. But I'm about to look into it
>> again. How are you guys measuring RMSD?
>>
>>
>>
>> On Wed, Jan 11, 2012 at 10:51 AM, Joshua Adelman <jla65.pitt.edu> wrote:
>>
>>> Hi Ross,
>>>
>>> On Jan 11, 2012, at 1:42 PM, Ross Walker wrote:
>>>
>>> > Hi Josh,
>>> >
>>> >> I would just add that I'm also very interested in seeing this bug
>>> >> resolved soon as well, and it would be great to know approximate
>>> >> timescales of when we might expect a patch. I'm not sure if having two
>>> >> users vs one interested in this shifts any priorities around, but I
>>> >> figured it couldn't hurt to suggest Marc isn't the only one interested
>>> >> in running CHAMBER generated systems using pmemd.cuda.
>>> >
>>> > The patch for this was made but looks like it needs more testing. I was
>>> > hoping to have that done by now but other things keep getting in the
>>> way.
>>> > The current plan is to focus on making sure it works for AMBER 12 and
>>> then
>>> > back porting a patch for AMBER 11.
>>> >
>>> > In the meantime the issue should only be affecting NPT calculations.
>>> You
>>> > could run the CPU version of the code to equilibrate the density with
>>> NPT
>>> > and then switch to NVT to use the CUDA code.
>>> >
>>>
>>> The only complication on our end with moving to NVT is that we're
>>> looking at conformational changes of a protein embedded in a membrane,
>>> which could result in the protein changing the volume it consumes in the
>>> bilayer. I would just be concerned that fixing the box dimensions could
>>> have unwanted consequences for either the protein or the lipids's behavior.
>>>
>>> I guess I'll just have to patiently wait for the testing to play itself
>>> out. Again it would be helpful to have a rough idea of timescales (weeks or
>>> months) you think it could reasonably take to make the patch public.
>>>
>>> Thanks again for your insight.
>>>
>>> Josh
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Thu Jan 12 2012 - 08:00:02 PST
